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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Ligand Binding and Linkage

Ligand Binding and Linkage

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Cell Aggregation Assays to Evaluate the Binding of the Drosophila Notch with Trans-Ligands and its Inhibition by Cis-Ligands

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GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm.

José-Emilio Sánchez-Aparicio¹, Giuseppe Sciortino¹, Daniel Viladrich Herrmannsdoerfer¹

¹Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.

International Journal of Molecular Sciences

|July 3, 2019

Summary

GPathFinder software simulates atomistic ligand diffusion pathways, enhancing protein-ligand docking by revealing binding dynamics. This open-source tool identifies known and novel binding routes, advancing drug and enzyme design.

Keywords:

computational chemistry drug design ligand diffusion molecular docking molecular modeling multi-objective genetic algorithm

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Area of Science:

Computational Chemistry
Structural Biology
Molecular Dynamics

Background:

Protein-ligand docking predicts binding poses but lacks dynamic insights.
Binding dynamics are crucial for affinity and selectivity.
Existing methods do not fully capture ligand entry/exit pathways.

Purpose of the Study:

Introduce GPathFinder, an open-source software for simulating ligand diffusion pathways.
Extend the capabilities of protein-ligand docking with dynamic simulation.
Provide a tool for understanding ligand-protein binding mechanisms.

Main Methods:

GPathFinder simulates ligand diffusion at the atomistic level.
It is built as an extension of the GaudiMM platform.
The method was benchmarked on 20 systems with known or suggested binding routes.

Main Results:

GPathFinder successfully identified known ligand-binding channels across 20 benchmark systems.
The software revealed novel, low-energy binding pathways in several cases.
Case studies demonstrated the practical utility of GPathFinder.

Conclusions:

GPathFinder offers a balance of accuracy and computational efficiency.
It enhances protein-ligand docking by incorporating binding pathway dynamics.
The software has significant implications for drug discovery and enzyme engineering.